Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin

Guan Wang; Traci Kitaoka; Ali Crawford; Qian Mao; Andrew Hesketh; Fergus Guppy; Garrett I. Ash; Jason  Liu; Mark  Gerstein; Yannis Pitsiladis

doi:10.1038/s41598-021-00608-9

Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin

Guan Wang, Traci Kitaoka, Ali Crawford, Qian Mao, Andrew Hesketh, Fergus Guppy, Garrett I. Ash, Jason Liu, Mark Gerstein, Yannis Pitsiladis

Research output: Contribution to journal › Article › peer-review

Abstract

RNA-seq has matured and become an important tool for studying RNA biology. Here we compared two RNA-seq (MGI DNBSEQ and Illumina NextSeq 500) and two microarray platforms (GeneChip Human Transcriptome Array 2.0 and Illumina Expression BeadChip) in healthy individuals administered recombinant human erythropoietin for transcriptome-wide quantification of differential gene expression. The results show that total RNA DNB-seq generated a multitude of target genes compared to other platforms. Pathway enrichment analyses revealed genes correlate to not only erythropoiesis and oxygen transport but also a wide range of other functions, such as tissue protection and immune regulation. This study provides a knowledge base of genes relevant to EPO biology through cross-platform comparisons and validation.

Original language	English
Article number	21705
Journal	Scientific Reports
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41598-021-00608-9
Publication status	Published - 4 Nov 2021

Bibliographical note

Funding Information:
We thank BGI Hong Kong for conducting the DNB-seq. This work was funded by the World Anti-Doping Agency (WADA) grant no. 08C19YP and ISF15E10YP to YPP. GIA was supported by a fellowship from the Office of Academic Affiliations at the United States Veterans Health Administration.

Keywords

MGI DNB-seq
Illumina mRNA-seq
GeneChip Human Transcriptome Array 2.0
Illumina Expression BeadChip
Recombinant human erythropoietin
Differential gene expression
Biological pathways

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Cite this

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title = "Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin",

abstract = "RNA-seq has matured and become an important tool for studying RNA biology. Here we compared two RNA-seq (MGI DNBSEQ and Illumina NextSeq 500) and two microarray platforms (GeneChip Human Transcriptome Array 2.0 and Illumina Expression BeadChip) in healthy individuals administered recombinant human erythropoietin for transcriptome-wide quantification of differential gene expression. The results show that total RNA DNB-seq generated a multitude of target genes compared to other platforms. Pathway enrichment analyses revealed genes correlate to not only erythropoiesis and oxygen transport but also a wide range of other functions, such as tissue protection and immune regulation. This study provides a knowledge base of genes relevant to EPO biology through cross-platform comparisons and validation.",

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note = "Funding Information: We thank BGI Hong Kong for conducting the DNB-seq. This work was funded by the World Anti-Doping Agency (WADA) grant no. 08C19YP and ISF15E10YP to YPP. GIA was supported by a fellowship from the Office of Academic Affiliations at the United States Veterans Health Administration.",

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doi = "10.1038/s41598-021-00608-9",

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AU - Wang, Guan

AU - Kitaoka, Traci

AU - Crawford, Ali

AU - Mao, Qian

AU - Hesketh, Andrew

AU - Guppy, Fergus

AU - Ash, Garrett I.

AU - Liu, Jason

AU - Gerstein, Mark

AU - Pitsiladis, Yannis

N1 - Funding Information: We thank BGI Hong Kong for conducting the DNB-seq. This work was funded by the World Anti-Doping Agency (WADA) grant no. 08C19YP and ISF15E10YP to YPP. GIA was supported by a fellowship from the Office of Academic Affiliations at the United States Veterans Health Administration.

PY - 2021/11/4

Y1 - 2021/11/4

N2 - RNA-seq has matured and become an important tool for studying RNA biology. Here we compared two RNA-seq (MGI DNBSEQ and Illumina NextSeq 500) and two microarray platforms (GeneChip Human Transcriptome Array 2.0 and Illumina Expression BeadChip) in healthy individuals administered recombinant human erythropoietin for transcriptome-wide quantification of differential gene expression. The results show that total RNA DNB-seq generated a multitude of target genes compared to other platforms. Pathway enrichment analyses revealed genes correlate to not only erythropoiesis and oxygen transport but also a wide range of other functions, such as tissue protection and immune regulation. This study provides a knowledge base of genes relevant to EPO biology through cross-platform comparisons and validation.

AB - RNA-seq has matured and become an important tool for studying RNA biology. Here we compared two RNA-seq (MGI DNBSEQ and Illumina NextSeq 500) and two microarray platforms (GeneChip Human Transcriptome Array 2.0 and Illumina Expression BeadChip) in healthy individuals administered recombinant human erythropoietin for transcriptome-wide quantification of differential gene expression. The results show that total RNA DNB-seq generated a multitude of target genes compared to other platforms. Pathway enrichment analyses revealed genes correlate to not only erythropoiesis and oxygen transport but also a wide range of other functions, such as tissue protection and immune regulation. This study provides a knowledge base of genes relevant to EPO biology through cross-platform comparisons and validation.

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JO - Scientific Reports

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ER -

Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin

Abstract

Bibliographical note

Keywords

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